[open-science] PLOS ONE offers Registered Reports

Peter Murray-Rust pm286 at cam.ac.uk
Wed Jan 15 09:24:10 UTC 2020

On Tue, Jan 14, 2020 at 10:44 PM David Knutson <dknutson at plos.org> wrote:

> PLOS today announced that *PLOS ONE* <https://journals.plos.org/plosone/>
> will soon offer a new preregistration article type,
> <https://www.plos.org/preregistration> Registered Reports.
> This is a useful step forward in principle.

However most reports of studies and reviews in the scholarly literature,
including PLOS, are not machine-processable or validatable.  (I have looked
at the first PLOS article I found and the tables are published as bitmaps
doi: https://doi.org/10.1371/journal.pone.0226983.t001  It is important
that machines can determine whether a preregistration is compliant and
whether the ontology is Open. So I have some technical
* are there other bodies (e.g. scientific societies or other publishers)
who have been involved in designing the structure and ontology of PLOS
preregistrations? Without those we get a plethora of publisher-specific
protocols, probably weakly designed.
* is there a published Open ontology/dictionary of terms and data
* are there semantic machine-accessible tools for validating subsequent
reports against the preregistration ("did they do what they said they

I spend a lot of time writing software to extract data from PDFs and
bitmaps because the publication-process destroys most semantic data. It
*is* possible to do a proper job as the International Union of
Crystallography has done for 30 years with its CIF standard. (
https://www.iucr.org/resources/cif)  - disclaimer, I am on the Advisory
Ctte. The first step is publicly agreed ontology/metadata which I hope
already exists.

"I always retain copyright in my papers, and nothing in any contract I sign
with any publisher will override that fact. You should do the same".

Peter Murray-Rust
Reader Emeritus in Molecular Informatics
Unilever Centre, Dept. Of Chemistry
University of Cambridge
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